SMTL ID : 3iae.1

Structure of benzaldehyde lyase A28S mutant with benzoylphosphonate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x D7K: 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(S)-hydroxy[(R)-hydroxy(methoxy)phosphoryl]phenylmethyl}-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium(Non-covalent)

D7K.1: 32 residues within 4Å: Chain A: G.393, A.394, L.395, T.396, Y.397, G.419, S.420, M.421, G.447, D.448, G.449, S.450, Y.453, N.475, S.477, W.478, G.479, A.480, T.481 Chain B: L.25, H.26, G.27, S.28, H.29, E.50, T.73, G.76, G.77, N.80, L.112, Q.113 Ligands: CA.2 26 PLIP interactions: 16 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:Y.397, A:W.478, A:W.478, A:A.480, B:L.25, B:T.73, B:L.112 Hydrogen bonds: A:A.394, A:L.395, A:T.396, A:G.419, A:M.421, A:G.447, A:G.447, A:G.449, A:S.450, A:N.475, A:G.479, A:A.480, B:S.28, B:S.28, B:Q.113, B:Q.113 Water bridges: B:H.29, B:G.77, B:G.77 D7K.3: 31 residues within 4Å: Chain A: H.26, G.27, S.28, H.29, E.50, T.73, G.76, G.77, N.80, L.112, Q.113 Chain B: G.393, A.394, L.395, T.396, Y.397, G.419, S.420, M.421, G.447, D.448, G.449, S.450, Y.453, N.475, S.477, W.478, G.479, A.480, T.481 Ligands: CA.4 23 PLIP interactions: 8 interactions with chain A, 15 interactions with chain B Hydrophobic interactions: A:T.73, A:L.112, B:Y.453, B:W.478, B:W.478, B:A.480 Hydrogen bonds: A:S.28, A:S.28, A:Q.113, B:L.395, B:T.396, B:G.419, B:M.421, B:D.448, B:G.449, B:S.450, B:N.475, B:G.479, B:A.480 Water bridges: A:H.29, A:G.77, A:Q.113, B:N.475 D7K.5: 32 residues within 4Å: Chain C: G.393, A.394, L.395, T.396, Y.397, G.419, S.420, M.421, G.447, D.448, G.449, S.450, Y.453, N.475, S.477, W.478, G.479, A.480, T.481 Chain D: L.25, H.26, G.27, S.28, H.29, E.50, T.73, G.76, G.77, N.80, L.112, Q.113 Ligands: CA.6 29 PLIP interactions: 18 interactions with chain C, 11 interactions with chain D Hydrophobic interactions: C:Y.397, C:W.478, C:W.478, C:A.480, D:L.25, D:T.73, D:L.112 Hydrogen bonds: C:A.394, C:L.395, C:T.396, C:T.396, C:G.419, C:M.421, C:G.447, C:G.447, C:G.449, C:S.450, C:Y.453, C:N.475, C:G.479, C:A.480, D:S.28, D:S.28, D:H.29, D:Q.113, D:Q.113 Water bridges: D:H.29, D:G.77, D:G.77 D7K.7: 31 residues within 4Å: Chain C: H.26, G.27, S.28, H.29, E.50, T.73, G.76, G.77, N.80, L.112, Q.113 Chain D: G.393, A.394, L.395, T.396, Y.397, G.419, S.420, M.421, G.447, D.448, G.449, S.450, Y.453, N.475, S.477, W.478, G.479, A.480, T.481 Ligands: CA.8 25 PLIP interactions: 16 interactions with chain D, 9 interactions with chain C Hydrophobic interactions: D:Y.453, D:W.478, D:W.478, D:A.480, C:T.73, C:L.112 Hydrogen bonds: D:L.395, D:T.396, D:T.396, D:G.419, D:M.421, D:D.448, D:G.449, D:S.450, D:N.475, D:N.475, D:G.479, D:A.480, C:S.28, C:S.28, C:H.29, C:Q.113 Water bridges: C:H.29, C:G.77, C:Q.113

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 7 residues within 4Å: Chain A: T.396, G.447, D.448, M.473, N.475, S.477 Ligands: D7K.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.448, A:M.473 CA.4: 6 residues within 4Å: Chain B: G.447, D.448, M.473, N.475, S.477 Ligands: D7K.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.448, B:M.473 CA.6: 7 residues within 4Å: Chain C: T.396, G.447, D.448, M.473, N.475, S.477 Ligands: D7K.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.448, C:M.473 CA.8: 6 residues within 4Å: Chain D: G.447, D.448, M.473, N.475, S.477 Ligands: D7K.7 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.448, D:M.473

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brandt, G.S. et al., Active-site engineering of benzaldehyde lyase shows that a point mutation can confer both new reactivity and susceptibility to mechanism-based inhibition. J.Am.Chem.Soc. (2010)

Release Date

2010-03-02

Peptides

Benzaldehyde lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Benzaldehyde lyase

Related Entries With Identical Sequence